# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 08:48:37 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-{[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]methyl}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(SCc3ccc(cc3)C#N)nc2C(=O)N1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 YH2  YH2  4-{[(2-amino-6-oxo-6,9-dihydro-1H-purin-8-yl)sulfanyl]methyl}benzonitrile  ligand  31  21  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YH2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 YH2  C01  C  CR6   0   0.493   3.9367  -1.5285   0.0183
 YH2  N02  N  NR16  0  -0.722   5.1912  -0.9036   0.0037
 YH2  C03  C  CR6   0   0.689   5.4219   0.4408  -0.0267
 YH2  N04  N  N     0  -0.503   4.4588   1.3299  -0.0437
 YH2  C05  C  CR56  0   0.482   3.2378   0.7806  -0.0335
 YH2  C06  C  CR56  0  -0.083   2.8968  -0.5583  -0.0042
 YH2  O07  O  O     0  -0.477   3.8505  -2.7455   0.0464
 YH2  N08  N  NH2   0  -0.832   6.7018   0.8393  -0.0774
 YH2  N09  N  NR15  0  -0.685   2.0517   1.4445  -0.0457
 YH2  C10  C  CR5   0   0.291   1.0648   0.4942  -0.0235
 YH2  N11  N  N     0  -0.442   1.5307  -0.7161   0.0014
 YH2  S12  S  S2    0   0.070  -0.6129   0.9692  -0.0295
 YH2  C13  C  CH2   0  -0.622  -1.3925  -0.6788   0.0056
 YH2  C14  C  CR6   0   0.107  -2.8740  -0.4584   0.0048
 YH2  C15  C  CR16  0  -0.270  -3.5645  -0.3355  -1.1983
 YH2  C16  C  CR16  0  -0.223  -4.9291  -0.1103  -1.2076
 YH2  C17  C  CR6   0  -0.005  -5.6134  -0.0025   0.0028
 YH2  C18  C  CR16  0  -0.223  -4.9325  -0.1194   1.2140
 YH2  C19  C  CR16  0  -0.271  -3.5675  -0.3438   1.2067
 YH2  C20  C  CSP   0   0.058  -7.0222   0.2266   0.0018
 YH2  N21  N  NS    0  -0.250  -8.1594   0.4120   0.0010
 YH2  H1   H  HNR6  0   0.425   5.9881  -1.5273   0.0103
 YH2  H2   H  HNH2  0   0.414   7.4483   0.2089   0.1617
 YH2  H3   H  HNH2  0   0.412   6.8870   1.8194   0.0540
 YH2  H4   H  HNR5  0   0.426   1.9328   2.4466  -0.0628
 YH2  H6   H  HCH2  0   0.309  -1.0680  -1.2389  -0.8699
 YH2  H7   H  HCH2  0   0.309  -1.0639  -1.2033   0.9012
 YH2  H8   H  HCR6  0   0.276  -3.0318  -0.4230  -2.1368
 YH2  H9   H  HCR6  0   0.285  -5.4616  -0.0188  -2.1443
 YH2  H10  H  HCR6  0   0.285  -5.4674  -0.0357   2.1501
 YH2  H11  H  HCR6  0   0.276  -3.0373  -0.4381   2.1458

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 YH2  N08  C03  single    1.341  0.020  1.341
 YH2  N04  C03  double    1.311  0.020  1.311
 YH2  N04  C05  single    1.339  0.020  1.339
 YH2  C03  N02  single    1.364  0.020  1.364
 YH2  C05  N09  aromatic  1.359  0.020  1.359
 YH2  C05  C06  aromatic  1.382  0.020  1.382
 YH2  N02  C01  single    1.402  0.020  1.402
 YH2  N09  C10  aromatic  1.370  0.020  1.370
 YH2  C06  C01  single    1.422  0.020  1.422
 YH2  C06  N11  aromatic  1.375  0.020  1.375
 YH2  C01  O07  double    1.220  0.020  1.220
 YH2  N21  C20  triple    1.152  0.020  1.152
 YH2  C10  N11  aromatic  1.297  0.020  1.297
 YH2  C10  S12  single    1.744  0.020  1.744
 YH2  C20  C17  single    1.427  0.020  1.427
 YH2  S12  C13  single    1.823  0.020  1.823
 YH2  C18  C17  aromatic  1.394  0.020  1.394
 YH2  C18  C19  aromatic  1.383  0.020  1.383
 YH2  C17  C16  aromatic  1.395  0.020  1.395
 YH2  C19  C14  aromatic  1.392  0.020  1.392
 YH2  C16  C15  aromatic  1.383  0.020  1.383
 YH2  C14  C15  aromatic  1.393  0.020  1.393
 YH2  C14  C13  single    1.498  0.020  1.498
 YH2  N02  H1   single    0.860  0.020  1.020
 YH2  N08  H2   single    0.890  0.020  1.040
 YH2  N08  H3   single    0.890  0.020  1.040
 YH2  N09  H4   single    0.860  0.020  1.020
 YH2  C13  H6   single    0.970  0.020  1.090
 YH2  C13  H7   single    0.970  0.020  1.090
 YH2  C15  H8   single    0.930  0.020  1.080
 YH2  C16  H9   single    0.930  0.020  1.080
 YH2  C18  H10  single    0.930  0.020  1.080
 YH2  C19  H11  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 YH2  O07  C01  C06  128.97  3.000
 YH2  O07  C01  N02  120.53  3.000
 YH2  C06  C01  N02  110.50  3.000
 YH2  H1   N02  C03  118.31  3.000
 YH2  H1   N02  C01  115.47  3.000
 YH2  C03  N02  C01  126.22  3.000
 YH2  N08  C03  N04  119.94  3.000
 YH2  N04  C03  N02  122.98  3.000
 YH2  N08  C03  N02  117.06  3.000
 YH2  C05  N04  C03  113.06  3.000
 YH2  N09  C05  C06  104.96  3.000
 YH2  C06  C05  N04  128.51  3.000
 YH2  N09  C05  N04  126.53  3.000
 YH2  N11  C06  C05  110.88  3.000
 YH2  N11  C06  C01  130.39  3.000
 YH2  C05  C06  C01  118.74  3.000
 YH2  H3   N08  H2   116.29  3.000
 YH2  H3   N08  C03  117.39  3.000
 YH2  H2   N08  C03  120.86  3.000
 YH2  H4   N09  C10  127.16  3.000
 YH2  H4   N09  C05  126.01  3.000
 YH2  C10  N09  C05  106.83  3.000
 YH2  S12  C10  N11  126.86  3.000
 YH2  S12  C10  N09  120.27  3.000
 YH2  N11  C10  N09  112.88  3.000
 YH2  C10  N11  C06  104.46  3.000
 YH2  C13  S12  C10   99.50  3.000
 YH2  H7   C13  H6   108.89  3.000
 YH2  H7   C13  C14  111.71  3.000
 YH2  H6   C13  C14  111.72  3.000
 YH2  H7   C13  S12  108.79  3.000
 YH2  H6   C13  S12  108.79  3.000
 YH2  C14  C13  S12  106.85  3.000
 YH2  C19  C14  C15  119.44  3.000
 YH2  C15  C14  C13  120.25  3.000
 YH2  C19  C14  C13  120.28  3.000
 YH2  H8   C15  C16  119.52  3.000
 YH2  H8   C15  C14  119.86  3.000
 YH2  C16  C15  C14  120.62  3.000
 YH2  H9   C16  C17  120.25  3.000
 YH2  H9   C16  C15  120.35  3.000
 YH2  C17  C16  C15  119.40  3.000
 YH2  C20  C17  C18  119.74  3.000
 YH2  C18  C17  C16  120.52  3.000
 YH2  C20  C17  C16  119.74  3.000
 YH2  H10  C18  C19  120.35  3.000
 YH2  H10  C18  C17  120.25  3.000
 YH2  C19  C18  C17  119.40  3.000
 YH2  H11  C19  C18  119.53  3.000
 YH2  H11  C19  C14  119.85  3.000
 YH2  C18  C19  C14  120.62  3.000
 YH2  N21  C20  C17  180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 YH2  CONST_01  N11  C10  N09  C05    0.00   0.0  0
 YH2  CONST_02  C10  N11  C06  C05    0.00   0.0  0
 YH2  CONST_03  C10  N09  C05  C06    0.00   0.0  0
 YH2  CONST_04  N09  C10  N11  C06    0.00   0.0  0
 YH2  CONST_05  N11  C06  C05  N09    0.00   0.0  0
 YH2  CONST_06  C17  C18  C19  C14    0.00   0.0  0
 YH2  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 YH2  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 YH2  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 YH2  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 YH2  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 YH2  CONST_12  N04  C03  N02  C01    0.00   0.0  0
 YH2  CONST_13  C05  N04  C03  N02    0.00   0.0  0
 YH2  CONST_14  C06  C01  N02  C03    0.00   0.0  0
 YH2  CONST_15  S12  C10  N09  C05  180.00   0.0  0
 YH2  CONST_16  S12  C10  N11  C06  180.00   0.0  0
 YH2  CONST_17  C18  C19  C14  C13  180.00   0.0  0
 YH2  CONST_18  C16  C15  C14  C13  180.00   0.0  0
 YH2  CONST_19  C20  C17  C16  C15  180.00   0.0  0
 YH2  CONST_20  C20  C17  C18  C19  180.00   0.0  0
 YH2  CONST_21  N08  C03  N02  C01  180.00   0.0  0
 YH2  CONST_22  O07  C01  N02  C03  180.00   0.0  0
 YH2  CONST_23  N08  C03  N04  C05  180.00   0.0  0
 YH2  CONST_24  H4   N09  C05  N04    0.00   0.0  0
 YH2  CONST_25  H10  C18  C19  C14  180.00   0.0  0
 YH2  CONST_26  H9   C16  C15  C14  180.00   0.0  0
 YH2  CONST_27  H11  C19  C14  C15  180.00   0.0  0
 YH2  CONST_28  H8   C15  C16  C17  180.00   0.0  0
 YH2  CONST_29  H1   N02  C03  N04  180.00   0.0  0
 YH2  CONST_31  H3   N08  C03  N02  180.00   0.0  0
 YH2  Var_01    C14  C13  S12  C10  179.98  30.0  3
 YH2  Var_02    C19  C14  C13  S12  -90.62  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 YH2  plan-1  C13  0.020
 YH2  plan-1  C14  0.020
 YH2  plan-1  C15  0.020
 YH2  plan-1  C16  0.020
 YH2  plan-1  C17  0.020
 YH2  plan-1  C18  0.020
 YH2  plan-1  C19  0.020
 YH2  plan-1  C20  0.020
 YH2  plan-1  N21  0.020
 YH2  plan-1  H8   0.020
 YH2  plan-1  H9   0.020
 YH2  plan-1  H10  0.020
 YH2  plan-1  H11  0.020
 YH2  plan-2  C01  0.020
 YH2  plan-2  N02  0.020
 YH2  plan-2  C03  0.020
 YH2  plan-2  N04  0.020
 YH2  plan-2  C05  0.020
 YH2  plan-2  C06  0.020
 YH2  plan-2  O07  0.020
 YH2  plan-2  N08  0.020
 YH2  plan-2  N09  0.020
 YH2  plan-2  C10  0.020
 YH2  plan-2  N11  0.020
 YH2  plan-2  S12  0.020
 YH2  plan-2  H1   0.020
 YH2  plan-2  H2   0.020
 YH2  plan-2  H3   0.020
 YH2  plan-2  H4   0.020

